Improving sensitivity of XANES structural fit to the bridged metal-metal coordination

Hard X-ray absorption spectroscopy is a valuable in situ probe for non-destructive diagnostics of metal sites. The low-energy interval of a spectrum (XANES) contains information about the metal oxidation state, ligand type, symmetry and distances in the first coordination shell but shows almost no dependency on the bridged metal-metal bond length. The higher-energy interval (EXAFS), on the contrary, is more sensitive to the coordination numbers and can decouple the contribution from distances in different coordination shells. Supervised machine-learning methods can combine information from different intervals of a spectrum; however, computational approaches for the near-edge region of the spectrum and higher energies are different. This work aims to keep all benefits of XANES and extend its sensitivity towards the interatomic distances in the first and second coordination shells. Using a binuclear bridged copper complex as a case study and cross-validation analysis as a quantitative tool it is shown that the first 170 eV above the edge are already sufficient to balance the contributions of Cu-O/N scattering and Cu-Cu scattering. As a more general outcome this work highlights the trivial but often overlooked importance of using `longer' energy intervals of XANES for structural refinement and machine-learning predictions. The first 200 eV above the absorption edge still do not require parametrization of Debye-Waller damping and can be calculated within full multiple scattering or finite difference approximations with only moderately increased computational costs.

Isomerism of CH 2 SO : Accurate structural, energetic, and spectroscopic characterization

A recent work [Ye et al. Mon. Not. R. Astron. Soc. 2023, 525, 1158] on the gas-phase formation of t-HC(O)SH, already detected in the interstellar medium, pointed out that the trans form of HC(S)OH is a potential candidate for astronomical observations. Prompted by these results, theCH 2 SO family of isomers has been investigated from an energetic point of view using a double-hybrid density functional in combination with a partially augmented triple-zeta basis set. This preliminary study showed that the most stable species of the family are the cis and trans forms of HC(O)SH and HC(S)OH. For their structural and spectroscopic characterization, a composite scheme based on coupled cluster (CC) calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects has been employed. This approach opens to the prediction of rotational constants with an accuracy of 0.1%. A hybrid scheme, based on harmonic frequencies computed using the CC singles, doubles and a perturbative treatment of triples method (CCSD(T)) in conjunction with a quadruple-zeta basis set, allowed us to obtain fundamental vibrational frequencies with a mean absolute error of about 1%.

Molecular Dynamics of Steroidal Rotors Probed by Theoretical, Spectroscopic and Dielectric Methods

Our study focuses on molecular rotors with fast-moving rotators and their potential applications in the development of new amphidynamic crystals. Steroidal molecular rotors with a dipolar fluorine-substituted phenyl group as the rotator were synthesized and characterized. Three different rotors were investigated with varying numbers of fluorine atoms. A comprehensive analysis was performed using vibrational spectroscopy (Raman, FT-IR), electronic circular dichroism (ECD), and dielectric response to understand the behavior of the investigated model rotors. The results were supported by theoretical calculations using Density Functional Theory (DFT) methods. The angle-dependent polarized Raman spectra confirmed the crystallinity of the samples. Nearly frequency and temperature-independent permittivity suggest low-frequency librational motion of stators. An in-depth analysis of ECD spectra revealed high conformational flexibility in solution, resulting in low ECD effects, while in the solid-state with restricted rotation, significant ECD effects were observed. These findings shed light on the conformational behavior and potential applications of the studied steroidal molecular rotors.

Laser-Induced Plasmas of Plutonium Dioxide in a Double-Walled Cell

Plutonium research has been stifled by the significant number of administrative controls and safety procedures, space and instrumentation limitations in radiological gloveboxes, and the potential for personnel and equipment contamination. To address the limited number of spectroscopic studies in Pu-bearing compounds in the current scientific literature, this work presents the use of double-walled cells (DWCs) in "clean" buildings/laboratories as an alternative to research in radiological gloveboxes. This study reports the first laser-induced breakdown spectroscopy (LIBS) experiments of a PuO2 pellet contained within a DWC, where the formation of elemental (atomic and ionic) species as well as the evolution from elemental to molecular products (PuxOy) was measured. Raman spectroscopy was also used to characterize the surface of the ablated pellet and the particulates deposited on the window of the inner cell. The full width half-maximum of the T2g band enabled us to obtain an estimate of the temperature at the pellet surface after the ablation pulse and the particulates based on the crystal lattice disorder. Particulates deposited on the window of the DWC during laser ablation were characterized using scanning electron microscopy, where molten irregular particulates and spheroids were observed. This exciting research conducted in a DWC describes our initial attempts to incorporate LIBS in the arsenal of spectroscopic tools for nuclear forensics applications.

Machine Learning-Assisted Classification of Paraffin-Embedded Brain Tumors with Raman Spectroscopy

Raman spectroscopy (RS) has demonstrated its utility in neurooncological diagnostics, spanning from intraoperative tumor detection to the analysis of tissue samples peri- and postoperatively. In this study, we employed Raman spectroscopy (RS) to monitor alterations in the molecular vibrational characteristics of a broad range of formalin-fixed, paraffin-embedded (FFPE) intracranial neoplasms (including primary brain tumors and meningiomas, as well as brain metastases) and considered specific challenges when employing RS on FFPE tissue during the routine neuropathological workflow. We spectroscopically measured 82 intracranial neoplasms on CaF2 slides (in total, 679 individual measurements) and set up a machine learning framework to classify spectral characteristics by splitting our data into training cohorts and external validation cohorts. The effectiveness of our machine learning algorithms was assessed by using common performance metrics such as AUROC and AUPR values. With our trained random forest algorithms, we distinguished among various types of gliomas and identified the primary origin in cases of brain metastases. Moreover, we spectroscopically diagnosed tumor types by using biopsy fragments of pure necrotic tissue, a task unattainable through conventional light microscopy. In order to address misclassifications and enhance the assessment of our models, we sought out significant Raman bands suitable for tumor identification. Through the validation phase, we affirmed a considerable complexity within the spectroscopic data, potentially arising not only from the biological tissue subjected to a rigorous chemical procedure but also from residual components of the fixation and paraffin-embedding process. The present study demonstrates not only the potential applications but also the constraints of RS as a diagnostic tool in neuropathology, considering the challenges associated with conducting vibrational spectroscopic analysis on formalin-fixed, paraffin-embedded (FFPE) tissue.

Endogenous Production and Vibrational Analysis of Heavy-Isotope-Labeled Peptides from Cyanobacteria

Stable isotope labeling is an extremely useful tool for characterizing the structure, tracing the metabolism, and imaging the distribution of natural products in living organisms using mass-sensitive measurement techniques. In this study, a cyanobacterium was cultured in 15 N/13 C-enriched media to endogenously produce labeled, bioactive oligopeptides. The extent of heavy isotope incorporation in these peptides was determined with LC-MS, while the overall extent of heavy isotope incorporation in whole cells was studied with nanoSIMS and AFM-IR. Up to 98 % heavy isotope incorporation was observed in labeled cells. Three of the most abundant peptides, microcystin-LR (MCLR), cyanopeptolin-A (CYPA), and aerucyclamide-A (ACAA), were isolated and further studied with Raman and FTIR spectroscopies and DFT calculations. This revealed several IR and Raman active vibrations associated with functional groups not common in ribosomal peptides, like diene, ester, thiazole, thiazoline, and oxazoline groups, which could be suitable for future vibrational imaging studies. More broadly, this study outlines a simple and relatively inexpensive method for producing heavy-labeled natural products. Manipulating the bacterial culture conditions by the addition of specific types and amounts of heavy-labeled nutrients provides an efficient means of producing heavy-labeled natural products for mass-sensitive imaging studies.

Exploring the Effect of V2O5 and Nb2O5 Content on the Structural, Thermal, and Electrical Characteristics of Sodium Phosphate Glasses and Glass-Ceramics

Na-V-P-Nb-based materials have gained substantial recognition as cathode materials in high-rate sodium-ion batteries due to their unique properties and compositions, comprising both alkali and transition metal ions, which allow them to exhibit a mixed ionic-polaronic conduction mechanism. In this study, the impact of introducing two transition metal oxides, V2O5 and Nb2O5, on the thermal, (micro)structural, and electrical properties of the 35Na2O-25V2O5-(40 - x)P2O5 - xNb2O5 system is examined. The starting glass shows the highest values of DC conductivity, σDC, reaching 1.45 × 10-8 Ω-1 cm-1 at 303 K, along with a glass transition temperature, Tg, of 371 °C. The incorporation of Nb2O5 influences both σDC and Tg, resulting in non-linear trends, with the lowest values observed for the glass with x = 20 mol%. Electron paramagnetic resonance measurements and vibrational spectroscopy results suggest that the observed non-monotonic trend in σDC arises from a diminishing contribution of polaronic conductivity due to the decrease in the relative number of V4+ ions and the introduction of Nb2O5, which disrupts the predominantly mixed vanadate-phosphate network within the starting glasses, consequently impeding polaronic transport. The mechanism of electrical transport is investigated using the model-free Summerfield scaling procedure, revealing the presence of mixed ionic-polaronic conductivity in glasses where x < 10 mol%, whereas for x ≥ 10 mol%, the ionic conductivity mechanism becomes prominent. To assess the impact of the V2O5 content on the electrical transport mechanism, a comparative analysis of two analogue series with varying V2O5 content (10 and 25 mol%) is conducted to evaluate the extent of its polaronic contribution.

Spontaneous Appearance of Triiodide Covering the Topmost Layer of the Iodide Solution Interface Without Photo-Oxidation

Ions containing iodine atoms at the vapor-aqueous solution interfaces critically affect aerosol growth and atmospheric chemistry due to their complex chemical nature and multivalency. While the surface propensity of iodide ions has been intensely discussed in the context of the Hofmeister series, the stability of various ions containing iodine atoms at the vapor-water interface has been debated. Here, we combine surface-specific sum-frequency generation (SFG) vibrational spectroscopy with ab initio molecular dynamics simulations to examine the extent to which iodide ions cover the aqueous surface. The SFG probe of the free O-D stretch mode of heavy water indicates that the free O-D group density decreases drastically at the interface when the bulk NaI concentration exceeds ∼2 M. The decrease in the free O-D group density is attributed to the spontaneous appearance of triiodide that covers the topmost interface rather than to the surface adsorption of iodide. This finding demonstrates that iodide is not surface-active, yet the highly surface-active triiodide is generated spontaneously at the water-air interface, even under dark and oxygen-free conditions. Our study provides an important first step toward clarifying iodine chemistry and pathways for aerosol formation.

Computational Assessment of Spectral Heterogeneity within Fresh Glioblastoma Tissue Using Raman Spectroscopy and Machine Learning Algorithms

Understanding and classifying inherent tumor heterogeneity is a multimodal approach, which can be undertaken at the genetic, biochemical, or morphological level, among others. Optical spectral methods such as Raman spectroscopy aim at rapid and non-destructive tissue analysis, where each spectrum generated reflects the individual molecular composition of an examined spot within a (heterogenous) tissue sample. Using a combination of supervised and unsupervised machine learning methods as well as a solid database of Raman spectra of native glioblastoma samples, we succeed not only in distinguishing explicit tumor areas-vital tumor tissue and necrotic tumor tissue can correctly be predicted with an accuracy of 76%-but also in determining and classifying different spectral entities within the histomorphologically distinct class of vital tumor tissue. Measurements of non-pathological, autoptic brain tissue hereby serve as a healthy control since their respective spectroscopic properties form an individual and reproducible cluster within the spectral heterogeneity of a vital tumor sample. The demonstrated decipherment of a spectral glioblastoma heterogeneity will be valuable, especially in the field of spectroscopically guided surgery to delineate tumor margins and to assist resection control.

Application of vibrational and fluorescence spectroscopy to the compositional analysis of colored-flesh potatoes

BACKGROUND

Determination of composition and physicochemical parameters of natural products requires dedicated, often laborious and expensive, analytical protocols. Different spectroscopic techniques, in conjunction with chemometrics, seem to have a considerable potential in direct analysis of raw plant material and foods, without any chemical treatment.

RESULTS

Fluorescence spectroscopy and three vibrational spectroscopy techniques were applied to determine total polyphenol content, antioxidant activity and macronutrient levels in red- and purple-fleshed potato varieties. Excitation-emission matrix fluorescence, Fourier transform Raman, attenuated total reflection Fourier transform infrared and near-infrared spectra were recorded for the freeze-dried samples. Combining spectral data and the results of reference analyses, partial least squares regression models were constructed for each parameter studied. For polyphenols and antioxidant activity, quantification errors found for validation samples amounted to 3.74-5.04% and 4.75-6.35%, respectively, whereas macronutrient analysis gave errors in the 3.45-4.55%, 3.09-5.30% and 5.10-8.58% ranges for starch, protein and sugar determinations, respectively.

CONCLUSION

The obtained results demonstrate that different spectroscopic techniques in combination with multivariate modeling allow simultaneous determination of various parameters of plant samples based on a single sample spectrum. They can effectively replace commonly used protocols of food product analysis requiring sample dissolving and extraction of the compounds of interest. © 2023 Society of Chemical Industry.

Exploring the Influence of the Phosphorus-Heteroatom Substitution in Nicotine on Its Electronic and Vibrational Spectroscopic Properties

The influence of phosphorus substitution of nitrogen in heterocyclic compounds on the vibrational spectroscopy as well as frontier molecular orbitals are analyzed. Nicotine with two nitrogen atoms in its structure is taken as the sample system to be studied computationally. By replacing the nitrogen atom in one or both rings of this molecule with phosphorus, three nicotine derivatives are created. The vibrational circular dichroism and infrared spectra of these four molecules in their monomer state, as well as the assemblies up to trimers are determined. The aforementioned spectra are calculated using static quantum chemical calculations employing a cluster-weighted approach. The calculated gas phase spectra of nicotine are compared to their respective experimental spectra. It is observed that the nicotine derivatives with phosphorus in the methylpyrrolidine ring have considerably different gas phase and bulk phase vibrational circular dichroism spectra when compared to nicotine. The phosphorus substitution reduces the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital as well as altering the polarizability and reactivity of the investigated molecules.

Cardiac multiscale bioimaging: from nano- through micro- to mesoscales

Cardiac multiscale bioimaging is an emerging field that aims to provide a comprehensive understanding of the heart and its functions at various levels, from the molecular to the entire organ. It combines both physiologically and clinically relevant dimensions: from nano- and micrometer resolution imaging based on vibrational spectroscopy and high-resolution microscopy to assess molecular processes in cardiac cells and myocardial tissue, to mesoscale structural investigations to improve the understanding of cardiac (patho)physiology. Tailored super-resolution deep microscopy with advanced proteomic methods and hands-on experience are thus strategically combined to improve the quality of cardiovascular research and support future medical decision-making by gaining additional biomolecular information for translational and diagnostic applications.

Gas-Phase Infrared Action Spectroscopy of CH2Cl+ and CH3ClH+: Likely Protagonists in Chlorine Astrochemistry

Two fundamental halocarbon ions, CH2Cl+ and CH3ClH+, were studied in the gas phase using the FELion 22-pole ion trap apparatus and the Free Electron Laser for Infrared eXperiments (FELIX) at Radboud University, Nijmegen (the Netherlands). The vibrational bands of a total of four isotopologs, CH235,37Cl+ and CH335,37ClH+, were observed in selected wavenumber regions between 500 and 2900 cm-1 and then spectroscopically assigned based on the results of anharmonic force field calculations performed at the CCSD(T) level of theory. As the infrared photodissociation spectroscopy scheme employed probes singly Ne-tagged weakly bound complexes, complementary quantum-chemical calculations of selected species were also performed. The impact of tagging on the vibrational spectra of CH2Cl+ and CH3ClH+ is found to be virtually negligible for most bands; for CH3ClH+-Ne, the observations suggest a proton-bound structural arrangement. The experimental band positions as well as the best estimate rotational molecular parameters given in this work provide a solid basis for future spectroscopic studies at high spectral resolutions.

Mastering Femtosecond Stimulated Raman Spectroscopy: A Practical Guide

Femtosecond stimulated Raman spectroscopy (FSRS) is a powerful nonlinear spectroscopic technique that probes changes in molecular and material structure with high temporal and spectral resolution. With proper spectral interpretation, this is equivalent to mapping out reactive pathways on highly anharmonic excited-state potential energy surfaces with femtosecond to picosecond time resolution. FSRS has been used to examine structural dynamics in a wide range of samples, including photoactive proteins, photovoltaic materials, plasmonic nanostructures, polymers, and a range of others, with experiments performed in multiple groups around the world. As the FSRS technique grows in popularity and is increasingly implemented in user facilities, there is a need for a widespread understanding of the methodology and best practices. In this review, we present a practical guide to FSRS, including discussions of instrumentation, as well as data acquisition and analysis. First, we describe common methods of generating the three pulses required for FSRS: the probe, Raman pump, and actinic pump, including a discussion of the parameters to consider when selecting a beam generation method. We then outline approaches for effective and efficient FSRS data acquisition. We discuss common data analysis techniques for FSRS, as well as more advanced analyses aimed at extracting small signals on a large background. We conclude with a discussion of some of the new directions for FSRS research, including spectromicroscopy. Overall, this review provides researchers with a practical handbook for FSRS as a technique with the aim of encouraging many scientists and engineers to use it in their research.

Identifying Chemical Differences in Cheddar Cheese Based on Maturity Level and Manufacturer Using Vibrational Spectroscopy and Chemometrics

Cheese is a nutritious dairy product and a valuable commodity. Internationally, cheddar cheese is produced and consumed in large quantities, and it is the main cheese variety that is exported from Australia. Despite its importance, the analytical methods to that are used to determine cheese quality rely on traditional approaches that require time, are invasive, and which involve potentially hazardous chemicals. In contrast, spectroscopic techniques can rapidly provide molecular information and are non-destructive, fast, and chemical-free methods. Combined with partner recognition methods (chemometrics), they can identify small changes in the composition or condition of cheeses. In this work, we combined FTIR and Raman spectroscopies with principal component analysis (PCA) to investigate the effects of aging in commercial cheddar cheeses. Changes in the amide I and II bands were the main spectral characteristics responsible for classifying commercial cheddar cheeses based on the ripening time and manufacturer using FTIR, and bands from lipids, including β'-polymorph of fat crystals, were more clearly determined through changes in the Raman spectra.

Synthesis and VCD Spectroscopic Characterization of a Series of Azacryptands from a Chiral Valine-Based Derivative of Tris(2-aminoethyl)amine (TREN)

Utilizing experimental and computational vibrational circular dichroism (VCD) spectroscopy, we explored the conformational preferences of a series of chiral C3 -symmetric octaazacryptands with tris(2-aminoethyl)-amine head groups derived from valine. While the spectra of the smallest azacryptand with p-phenyl linkers and its elongated derivative with p-biphenyls linker were found to match well with the computed spectra, the computed conformational preferences of the m-biphenyl-based azacryptand did not seem to reflect the conformations dominating in chloroform solution. A detailed analysis revealed that structural changes resulting in a collapsed cage structure gave a notably better match with the experiment. It could subsequently be concluded from the VCD analysis, that the octaazacryptands prefer a collapsed structure, which is not predicted by density functional theory (DFT) calculations as the global minimum structures. These findings are expected to have consequences also for future studies on inclusion complexes of such azacryptands.

Lipidomic profiling reveals phenotypic diversity and nutritional benefits in Ficus carica L. (Fig.) seed cultivars

Introduction

Ficus carica L. seeds are a substantial source of minor oil with high unsaturation levels and potent antioxidant properties. The study aims to evaluate the mineral composition, lipodomic profile, and vibrational fingerprints of 22 fig genotypes utilizing FTIR-ATR techniques and chemometrics.

Methods

FTIR-ATR spectroscopy and chemometric techniques were employed to examine the phenotypic diversity of fig seeds. The investigation was performed in detail. The research analyzed twenty-two fig genotypes to assess their nutritional properties, genetic relationships, and potential applications.

Results

The results demonstrate substantial nutritional benefits related to fig seeds, which could serve as genetic resources for selection programs for extracting vegetable oil and functional ingredients. Additionally, a detailed lipodomic profile analysis led to the categorization of the genotypes into four unique clusters. The study uncovered new insights regarding the nutritional composition of the samples, while also highlighting significant similarities and differences. The findings showcased the phenotypic diversity within the studied fig germplasm, which is likely attributed to underlying genetic factors. These accessions offer a valuable gene pool for future breeding programs and diverse applications involving fig seeds.

Discussion

This work contributes to the selection of potential genotypes for scientific and industrial purposes. Furthermore, the application of FTIR and chemometrics revealed a noteworthy diversity of patterns, emphasizing the previously underestimated significance of this aspect in evaluating the chemodiversity of the species.

Recent Trends of Vibrational Spectroscopy in Examination of Sequence of Strokes: Application in Forensic Documents Examination

Chronological sequencing of ink strokes has been a challenge for the Forensic Document Examiners (FDE). Document forgery is a common practice and the ability to determine the order in which the primary and the subsequent strokes have been made is crucial for establishing the authenticity of a document. Lately, the prime thrust of establishing the sequence of intersection of ink lines has shifted from an optical to an analytical approach. Several studies have been reported to explore the use of spectroscopic techniques in determining the sequence of ink strokes made using gel pen inks, ball pen inks, fountain inks, printed ink, stamp inks, etc. The present study aims to study the existing trends in examining the sequence of ink strokes or crossing of lines using vibrational spectroscopic techniques viz. Infrared and Raman Spectroscopy. Several interesting inferences have been drawn, such as factors like paper type and time gap between the application of two intersecting strokes does not influence the determination of the sequence of inter-crossing strokes. A trend of using two analytical techniques viz. VSC, AFM, HPTLC, TOF-SIMS, and SEM/EDX with vibrational spectroscopic techniques have been found to provide reliable results. The study also suggests future research directions in the field, aiming to address challenges faced by the FDEs and provide accurate and reliable solutions for document examination.

Point-of-care detection of fibrosis in liver transplant surgery using near-infrared spectroscopy and machine learning

Introduction

Visual assessment and imaging of the donor liver are inaccurate in predicting fibrosis and remain surrogates for histopathology. We demonstrate that 3-s scans using a handheld near-infrared-spectroscopy (NIRS) instrument can identify and quantify fibrosis in fresh human liver samples.

Methods

We undertook NIRS scans on 107 samples from 27 patients, 88 from 23 patients with liver disease, and 19 from four organ donors.

Results

Liver disease patients had a median immature fibrosis of 40% (interquartile range [IQR] 20-60) and mature fibrosis of 30% (10%-50%) on histopathology. The organ donor livers had a median fibrosis (both mature and immature) of 10% (IQR 5%-15%). Using machine learning, this study detected presence of cirrhosis and METAVIR grade of fibrosis with a classification accuracy of 96.3% and 97.2%, precision of 96.3% and 97.0%, recall of 96.3% and 97.2%, specificity of 95.4% and 98.0% and area under receiver operator curve of 0.977 and 0.999, respectively. Using partial-least square regression machine learning, this study predicted the percentage of both immature (R 2 = 0.842) and mature (R 2 = 0.837) with a low margin of error (root mean square of error of 9.76% and 7.96%, respectively).

Conclusion

This study demonstrates that a point-of-care NIRS instrument can accurately detect, quantify and classify liver fibrosis using machine learning.

Water bend-libration as a cellular Raman imaging probe of hydration

Water is a ubiquitous and vital component of living systems. Hydration, which is the interaction between water and intracellular biomolecules, plays an important role in cellular processes. However, it is technically challenging to study water structure within cells directly. Here, we demonstrate the utility and power of the water bend-libration combination band as a unique Raman spectral imaging probe of cellular hydration. Hydration maps reveal distinct water environments within subcellular compartments (e.g., nucleolus and lipid droplet) due to the spectral sensitivity of this coupled vibrational band. Spectroscopic studies using the water bend-libration are broadly applicable, offering the potential to capture the chemical complexity of hydration in numerous systems.

The Cyanido-Sulfate Anion [SO3 CN]. Chemistry 2023;29:e202301761. [PMID: 37431537 DOI: 10.1002/chem.202301761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The reaction of the pyridine adduct of SO3 and tetra-n-butyl-ammonium cyanide, [N(n Bu)4 ][CN] at room temperature leads to the unprecedented cyanido-sulfate anion [SO3 CN]- stabilized in the salt [N(n Bu)4 ][SO3 CN]. The anion is a pseudo-halogen congener of the well-known fluoro- and chloro-sulfates. The new anion has been studied by vibrational spectroscopy and theoretical calculations.

Comparison between Variable-Selection Algorithms in PLS Regression with Near-Infrared Spectroscopy to Predict Selected Metals in Soil

Soil is one of the Earth's most important natural resources. The presence of metals can decrease environmental quality if present in excessive amounts. Analyzing soil metal contents can be costly and time consuming, but near-infrared (NIR) spectroscopy coupled with chemometric tools can offer an alternative. The most important multivariate calibration method to predict concentrations or physical, chemical or physicochemical properties as a chemometric tool is partial least-squares (PLS) regression. However, a large number of irrelevant variables may cause problems of accuracy in the predictive chemometric models. Thus, stochastic variable-selection techniques, such as the Firefly algorithm by intervals in PLS (FFiPLS), can provide better solutions for specific problems. This study aimed to evaluate the performance of FFiPLS against deterministic PLS algorithms for the prediction of metals in river basin soils. The samples had their spectra collected from the region of 1000-2500 nm. Predictive models were then built from the spectral data, including PLS, interval-PLS (iPLS), successive projections algorithm for interval selection in PLS (iSPA-PLS), and FFiPLS. The chemometric models were built with raw data and preprocessed data by using different methods such as multiplicative scatter correction (MSC), standard normal variate (SNV), mean centering, adjustment of baseline and smoothing by the Savitzky-Golay method. The elliptical joint confidence region (EJCR) used in each chemometric model presented adequate fit. FFiPLS models of iron and titanium obtained a relative prediction deviation (RPD) of more than 2. The chemometric models for determination of aluminum obtained an RPD of more than 2 in the preprocessed data with SNV, MSC and baseline (offset + linear) and with raw data. The metals Be, Gd and Y failed to obtain adequate models in terms of residual prediction deviation (RPD). These results are associated with the low values of metals in the samples. Considering the complexity of the samples, the relative error of prediction (REP) obtained between 10 and 25% of the values adequate for this type of sample. Root mean square error of calibration and prediction (RMSEC and RMSEP, respectively) presented the same profile as the other quality parameters. The FFiPLS algorithm outperformed deterministic algorithms in the construction of models estimating the content of Al, Be, Gd and Y. This study produced chemometric models with variable selection able to determine metals in the Ipojuca River watershed soils using reflectance-mode NIR spectrometry.

Ab Initio Approach to the Structure, Vibrational Properties, and Electron Binding Energies of H2S∙∙∙SO2

The present study employs high-level ab initio calculations to investigate the structure, vibrational frequencies, and electronic properties of H2S∙∙∙SO2. The analysis of vibrational frequencies reveals an intramolecular vibrational energy transfer phenomenon, where energy from the stretching modes of H2S is transferred to the ν1s mode of SO2. At the CCSD(T)/aug-cc-pVQZ level, the interaction energy between H2S and SO2 is predicted to be 2.78 kcal/mol. Electron propagator theory calculations yield a HOMO-LUMO gap of 8.24 eV for H2S∙∙∙SO2. Furthermore, by utilizing ab initio results for the adiabatic ionization energy and electron affinity, the electrophilicity of H2S∙∙∙SO2 is estimated to be 2.01 eV. This value is similar to the electrophilicity of SO2, suggesting comparable reactivity and chemical behavior. The non-covalent interaction (NCI) analysis of the H2S∙∙∙SO2 complex emphasizes the significant contribution of non-covalent van der Waals interactions in its energetic stabilization.

Contribution of Dynamic Rheology Coupled to FTIR and Raman Spectroscopies to the Real-Time Shaping Ability of a Hyperbranched Polycarbosilane

In the field of non-oxide ceramics, the polymer-derived ceramic (PDC) approach appears to be very promising, especially for obtaining easily shaped and homogeneous materials in terms of structure and composition. However, in order to reach a suitable form during the process, it is often necessary to study the rheology of preceramic polymers while they are modified during polymerisation or crosslinking reactions. Given this need in the understanding of the real-time rheology of macromolecules during their synthesis, a rheometer coupled with both an infrared spectrometer and a Raman probe is described as a powerful tool for monitoring in situ synthesised polycarbosilanes. Indeed, this original device allows one to control the viscosity of a hyberbranched polycarbosilane from defined difunctional and tetrafunctional monomers. Meanwhile, it links this evolution to structural modifications in the macromolecular structure (molar masses, dispersity and conformation), based on SEC-MALS analyses, synchronised by the monomer conversion determined by using Raman and infrared spectroscopies, a common denominator of the aforementioned instrumental platform.

The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State

Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the P-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.

Effect of Solvent Polarity on the Spectral Characteristics of 5,10,15,20-Tetrakis(p-hydroxyphenyl)porphyrin

The electronic absorption and vibrational spectra of deprotonated 5,10,15,20-tetrakis(p-hydroxyphenyl)porphyrin (THPP) are studied as a function of solvent polarity in H₂O-DMF, H₂O-acetone, H₂O-methanol, and DMF-acetone mixtures. The maximum absorption wavelength (λ_max) of the lowest energy electronic absorption band of deprotonated THPP shows an unusual solvatochromism-a bathochromic followed by a hypsochromic shift with reduced polarity. According to the correlation analysis, both specific interactions (H-bonds) and nonspecific interactions affect the spectral changes of this porphyrin. Furthermore, the solvent polarity scale E_T(30) can explain both shifts very well. At higher polarity (E_T(30) > 48), THPP exists as a hyperporphyrin. The E_T(30) is linear with λ_max and a decrease in solvent polarity is accompanied by a bathochromic shift of λ_max. These results can be rationalized in terms of the cooperative effects of H-bonds and nonspecific interactions on the spectra of hyperporphyrin. At relatively low polarity (45.5 < E_T(30) < 48), hyperporphyrin gradually becomes Na₂P as E_T(30) reaches the critical value of 45.5. The spectrum of the hyperporphyrin turns into the three-band spectrum of the metalloporphyrin, which is accompanied by a hypsochromic shift of λ_max.

Low-Frequency Raman Spectroscopy of Pure and Cocrystallized Mycophenolic Acid

The aqueous solubility of solid-state pharmaceuticals can often be enhanced by cocrystallization with a coformer to create a binary cocrystal with preferred physical properties. Greater understanding of the internal and external forces that dictate molecular structure and intermolecular packing arrangements enables more efficient design of new cocrystals. Low-frequency (sub-200 cm^-1) Raman spectroscopy experiments and solid-state density functional theory simulations have been utilized together to investigate the crystal lattice vibrations of mycophenolic acid, an immunosuppressive drug, in its pure form and as a cocrystal with 2,2'-dipyridylamine. The lattice vibrations primarily consist of large-amplitude translations and rotations of the crystal components, thereby providing insights into the critical intermolecular forces governing cohesion of the molecular solids. The simulations reveal that despite mycophenolic acid having a significantly unfavorable conformation in the cocrystal as compared to the pure solid, the cocrystal exhibits greater thermodynamic stability over a wide temperature range. The energetic penalty due to the conformational strain is more than compensated for by the strong intermolecular forces between the drug and 2,2'-dipyridylamine. Quantifying the balance of internal and external energy factors in cocrystal formation indicates a path forward in the development of future mycophenolic acid cocrystals.

Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems

Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms.  This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Spectral Features Differentiate Aging-Induced Changes in Parchment-A Combined Approach of UV/VIS, µ-ATR/FTIR and µ-Raman Spectroscopy with Multivariate Data Analysis

From the moment of production, artworks are constantly exposed to changing environmental factors potentially inducing degradation. Therefore, detailed knowledge of natural degradation phenomena is essential for proper damage assessment and preservation. With special focus on written cultural heritage, we present a study on the degradation of sheep parchment employing accelerated aging with light (295-3000 nm) for one month, 30/50/80% relative humidity (RH) and 50 ppm sulfur dioxide with 30/50/80%RH for one week. UV/VIS spectroscopy detected changes in the sample surface appearance, showing browning after light-aging and increased brightness after SO₂-aging. Band deconvolution of ATR/FTIR and Raman spectra and factor analysis of mixed data (FAMD) revealed characteristic changes of the main parchment components. Spectral features for degradation-induced structural changes of collagen and lipids turned out to be different for the employed aging parameters. All aging conditions induced denaturation (of different degrees) indicated by changes in the secondary structure of collagen. Light treatment resulted in the most pronounced changes for collagen fibrils in addition to backbone cleavage and side chain oxidations. Additional increased disorder for lipids was observed. Despite shorter exposure times, SO₂-aging led to a weakening of protein structures induced by transitions of stabilizing disulfide bonds and side chain oxidations.

Molecular Fingerprint Detection Using Raman and Infrared Spectroscopy Technologies for Cancer Detection: A Progress Review

Molecular vibrations play a crucial role in physical chemistry and biochemistry, and Raman and infrared spectroscopy are the two most used techniques for vibrational spectroscopy. These techniques provide unique fingerprints of the molecules in a sample, which can be used to identify the chemical bonds, functional groups, and structures of the molecules. In this review article, recent research and development activities for molecular fingerprint detection using Raman and infrared spectroscopy are discussed, with a focus on identifying specific biomolecules and studying the chemical composition of biological samples for cancer diagnosis applications. The working principle and instrumentation of each technique are also discussed for a better understanding of the analytical versatility of vibrational spectroscopy. Raman spectroscopy is an invaluable tool for studying molecules and their interactions, and its use is likely to continue to grow in the future. Research has demonstrated that Raman spectroscopy is capable of accurately diagnosing various types of cancer, making it a valuable alternative to traditional diagnostic methods such as endoscopy. Infrared spectroscopy can provide complementary information to Raman spectroscopy and detect a wide range of biomolecules at low concentrations, even in complex biological samples. The article concludes with a comparison of the techniques and insights into future directions.

Lipidomics in food quality and authentication: A comprehensive review of novel trends and applications using chromatographic and spectroscopic techniques

Lipid analysis is an integral part of food authentication and quality control which provides consumers with the necessary information to make an informed decision about their lipid intake. Recent advancement in lipid analysis and lipidome scope represents great opportunities for food science. In this review we provide a comprehensive overview of available tools for extraction, analysis and interpretation of data related to dietary fats analyses. Different analytical platforms are discussed including GC, MS, NMR, IR and UV with emphasis on their merits and limitations alongside complementary tools such as chemometric models and lipid-targeted online databases. Applications presented here include quality control, authentication of organic and delicacy food, tracing dietary fat source and investigating the effect of heat/storage on lipids. A multitude of analytical methods with different sensitivity, affordability, reproducibility and ease of operation are now available to comprehensively analyze dietary fats. Application of these methods range from studies which favor the use of large data generating platforms such as MS-based methods, to routine quality control which demands easy to use affordable equipment as TLC and IR. Hence, this review provides a navigation tool for food scientists to help develop an optimal protocol for their future lipid analysis quest.

Challenges related to the application of analytical methods to control insect meals in the context of European legislation

Since their approval for use in aquaculture in 2017, processed insect proteins have been extensively studied for their nutritional quality in animal feed. This new type of meal is highly promising but requires, as for other products used in animal feed, strict sanitary control in accordance with European legislation. Within this legal framework, light microscopy and PCR remain the official methods but have some analytical limitations that other methods could overcome. This paper aims to provide an overview of the European legislation concerning use of processed insect proteins, but also to highlight the advantages and disadvantages of the official methods for their analysis. It also points out other analytical methods, which have already proved their worth for the analysis of processed animal proteins, which could be used as complementary methods.

The Degradation of Daguerreotypes and the Relationship with Their Multi-Material Structure: A Multimodal Investigation

Preserving and analytically examining daguerreotypes is particularly challenging because of their multi-material and multi-component structure. Various sensors have been exploited to examine mainly the image plates of the daguerreotypes even though the degradation goes beyond this component. Micro-analyses have been the preferred method due to the nanoscale structure of the image particles. In this work, we propose comprehensive multi-modal non-invasive sensing to investigate the corrosion products present in nine daguerreotypes from the Fondazione Alinari per la Fotografia (FAF, Florence, Italy). The methodology proposed includes chemical and morphological analyses: portable X-ray fluorescence spectrometry (pXRF), Raman microspectroscopy (μ-Raman), and micro-Fourier transform infrared spectroscopy in reflection mode (μ-rFTIR) for the chemical identification. For the first time, optical coherence tomography (OCT) was deployed to record the cross-sectional and morphological data of the relevant corrosion formations on daguerreotypes in a contactless way. The results allowed the characterization, in a non-invasive mode at a microscopic level, of a wide range of degradation products produced by the interaction of the different elements present in the structure of the daguerreotypes. The aim was to verify the performance of the proposed methodology and to link the chemical and physical complexity of the entire structure, disclosed by the state-of-art sensors, to the daguerreotype degradation. The results draw attention to the need to monitor not only the image condition but the whole object as a partially closed system in constant interaction internally and with the environment.

Detection and Quantification of Adulteration in Krill Oil with Raman and Infrared Spectroscopic Methods

Raman and infrared spectroscopy, used as individual and low-level fused datasets, were evaluated to identify and quantify the presence of adulterants (palm oil, PO; ω-3 concentrates in ethyl ester, O3C and fish oil, FO) in krill oil. These datasets were qualitatively analysed with principal component analysis (PCA) and classified as adulterated or unadulterated using support vector machines (SVM). Using partial least squares regression (PLSR), it was possible to identify and quantify the adulterant present in the KO mixture. Raman spectroscopy performed better (r² = 0.98; RMSEP = 2.3%) than IR spectroscopy (r² = 0.91; RMSEP = 4.2%) for quantification of O3C in KO. A data fusion approach further improved the analysis with model performance for quantification of PO (r² = 0.98; RMSEP = 2.7%) and FO (r² = 0.76; RMSEP = 9.1%). This study demonstrates the potential use of Raman and IR spectroscopy to quantify adulterants present in KO.

Chemical Feedback in the Self-Assembly and Function of Air-Liquid Interfaces: Insight into the Bottlenecks of CO2 Direct Air Capture

As fossil fuels remain a major source of energy throughout the world, developing efficient negative emission technologies, such as direct air capture (DAC), which remove carbon dioxide (CO₂) from the air, becomes critical for mitigating climate change. Although all DAC processes involve CO₂ transport from air into a sorbent/solvent, through an air-solid or air-liquid interface, the fundamental roles the interfaces play in DAC remain poorly understood. Herein, we study the interfacial behavior of amino acid (AA) solvents used in DAC through a combination of vibrational sum frequency generation spectroscopy and molecular dynamics simulations. This study revealed that the absorption of atmospheric CO₂ has antagonistic effects on subsequent capture events that are driven by changes in bulk pH and specific ion effects that feedback on surface organization and interactions. Among the three AAs (leucine, valine, and phenylalanine) studied, we identify and separate behaviors from CO₂ loading, chemical changes, variations in pH, and specific ion effects that tune structural and chemical degrees of freedom at the air-aqueous interface. The fundamental mechanistic findings described here are anticipated to enable new approaches to DAC based on exploiting interfaces as a tool to address climate change.

Near-infrared spectroscopy for structural bone assessment

Aims

Disorders of bone integrity carry a high global disease burden, frequently requiring intervention, but there is a paucity of methods capable of noninvasive real-time assessment. Here we show that miniaturized handheld near-infrared spectroscopy (NIRS) scans, operated via a smartphone, can assess structural human bone properties in under three seconds.

Methods

A hand-held NIR spectrometer was used to scan bone samples from 20 patients and predict: bone volume fraction (BV/TV); and trabecular (Tb) and cortical (Ct) thickness (Th), porosity (Po), and spacing (Sp).

Results

NIRS scans on both the inner (trabecular) surface or outer (cortical) surface accurately identified variations in bone collagen, water, mineral, and fat content, which then accurately predicted bone volume fraction (BV/TV, inner R² = 0.91, outer R² = 0.83), thickness (Tb.Th, inner R² = 0.9, outer R² = 0.79), and cortical thickness (Ct.Th, inner and outer both R² = 0.90). NIRS scans also had 100% classification accuracy in grading the quartile of bone thickness and quality.

Conclusion

We believe this is a fundamental step forward in creating an instrument capable of intraoperative real-time use.

Cite this article: Bone Jt Open 2023;4(4):250–261.

Surface-Enhanced Raman Analysis of Uric Acid and Hypoxanthine Analysis in Fractionated Bodily Fluids

In recent years, the disease burden of hyperuricemia has been increasing, especially in high-income countries and the economically developing world with a Western lifestyle. Abnormal levels of uric acid and hypoxanthine are associated with many diseases, and therefore, to demonstrate improved methods of uric acid and hypoxanthine detection, three different bodily fluids were analysed using surface-enhanced Raman spectroscopy (SERS) and high-performance liquid chromatography (HPLC). Gold nanostar suspensions were mixed with series dilutions of uric acid and hypoxanthine, 3 kDa centrifugally filtered human blood serum, urine and saliva. The results show that gold nanostars enable the quantitative detection of the concentration of uric acid and hypoxanthine in the range 5-50 μg/mL and 50-250 ng/mL, respectively. The peak areas of HPLC and maximum peak intensity of SERS have strongly correlated, notably with the peaks of uric acid and hypoxanthine at 1000 and 640 cm^-1, respectively. The r² is 0.975 and 0.959 for uric acid and hypoxanthine, respectively. Each of the three body fluids has a number of spectral features in common with uric acid and hypoxanthine. The large overlap of the spectral bands of the SERS of uric acid against three body fluids at spectra peaks were at 442, 712, 802, 1000, 1086, 1206, 1343, 1436 and 1560 cm^-1. The features at 560, 640, 803, 1206, 1290 and 1620 cm^-1 from hypoxanthine were common to serum, saliva and urine. There is no statistical difference between HPLC and SERS for determination of the concentration of uric acid and hypoxanthine (p > 0.05). For clinical applications, 3 kDa centrifugal filtration followed by SERS can be used for uric acid and hypoxanthine screening is, which can be used to reveal the subtle abnormalities enhancing the great potential of vibrational spectroscopy as an analytical tool. Our work supports the hypnosis that it is possible to obtain the specific concentration of uric acid and hypoxanthine by comparing the SER signals of serum, saliva and urine. In the future, the analysis of other biofluids can be employed to detect biomarkers for the diagnosis of systemic pathologies.

Phosphorus-Boron Multiple Bonding in the π Radical HBP

The HBP radical was generated via the reaction of laser ablated boron atom with PH₃ in a solid neon matrix, which is identified via IR spectroscopy with isotopic substitutions and quantum chemical calculations. The results show that HBP has a ² Π electronic ground state with a short B-P bond. Bonding analysis indicates that besides an electron-sharing σ bond, there are two degenerate π bonding orbitals that are occupied by three electrons, resulting in a bond order of two and half between P and B. This is in sharp contrast to the bonding properties of the isovalent HNB, which was characterized to be a N≡B triply bonded σ radical with the unpaired electron locating on the B atom.

Infrared Spectroscopy Evidence of Weak Interactions in Frustrated Lewis Pairs Formed by Tris(pentafluorophenyl)borane

Frustrated Lewis pairs (FLPs) have been widely investigated as promising catalysts due to their metal-free feature and ability to activate small molecules. Since their discovery, many works have been investigating how these Lewis pairs (intermolecular pairs) are held together in an encounter complex. This prompted several studies based on theoretical investigations, but experimental ones are limited yet. In this communication we show evidence of weak intermolecular interactions between Lewis acids and Lewis bases, distinguishing the Lewis adduct from FLPs, by probing fluorine-carbon vibrational modes using infrared spectroscopy. The main evidence is based on the band shifts occurring in FLPs due to weak hydrogen bonds between the hydrogen atoms of the Lewis base and the fluorine atoms of Lewis acid.

The First Alkaline-Earth Azidoaurate(III), Ba[Au(N3 )4 ]2 ⋅ 4 H2 O

Transparent, dark orange Ba[Au(N₃ )₄ ]₂  ⋅ 4 H₂ O was synthesized by reaction of Ba(N₃ )₂ and AuCl₃ or HAuCl₄ in aqueous solution. The novel barium tetraazidoaurate(III) tetrahydrate crystallizes in the monoclinic space group Cc (no. 9) with a=1813.68(17) pm, b=1737.95(11) pm, c=682.04(8) pm and β=108.849(4)°. The predominant structural features of Ba[Au(N₃ )₄ ]₂  ⋅ 4 H₂ O are two crystallographically independent discrete anions [Au(N₃ )₄ ]^- with gold in a tetragonal planar coordination by nitrogen. Vibrational spectra show good agreement with those of other azidoaurates(III). Upon drying, this salt was shown to be a highly explosive material.

Decoding the metabolic response of Escherichia coli for sensing trace heavy metals in water

Heavy metal contamination due to industrial and agricultural waste represents a growing threat to water supplies. Frequent and widespread monitoring for toxic metals in drinking and agricultural water sources is necessary to prevent their accumulation in humans, plants, and animals, which results in disease and environmental damage. Here, the metabolic stress response of bacteria is used to report the presence of heavy metal ions in water by transducing ions into chemical signals that can be fingerprinted using machine learning analysis of vibrational spectra. Surface-enhanced Raman scattering surfaces amplify chemical signals from bacterial lysate and rapidly generate large, reproducible datasets needed for machine learning algorithms to decode the complex spectral data. Classification and regression algorithms achieve limits of detection of 0.5 pM for As³⁺ and 6.8 pM for Cr⁶⁺, 100,000 times lower than the World Health Organization recommended limits, and accurately quantify concentrations of analytes across six orders of magnitude, enabling early warning of rising contaminant levels. Trained algorithms are generalizable across water samples with different impurities; water quality of tap water and wastewater was evaluated with 92% accuracy.

Single Crystals of EuScCuSe3: Synthesis, Experimental and DFT Investigations

EuScCuSe₃ was synthesized from the elements for the first time by the method of cesium-iodide flux. The crystal belongs to the orthorhombic system (Cmcm) with the unit cell parameters a = 3.9883(3) Å, b = 13.2776(9) Å, c = 10.1728(7) Å, V = 538.70(7) ų. Density functional (DFT) methods were used to study the crystal structure stability of EuScCuSe₃ in the experimentally obtained Cmcm and the previously proposed Pnma space groups. It was shown that analysis of elastic properties as Raman and infrared spectroscopy are powerless for this particular task. The instability of EuScCuSe₃ in space group Pnma space group is shown on the basis of phonon dispersion curve simulation. The EuScCuSe₃ can be assigned to indirect wide-band gap semiconductors. It exhibits the properties of a soft ferromagnet at temperatures below 2 K.

Experimental FTIR-MI and Theoretical Studies of Isocyanic Acid Aggregates

Homoaggregates of isocyanic acid (HNCO) were studied using FTIR spectroscopy combined with a low-temperature matrix isolation technique and quantum chemical calculations. Computationally, the structures of the HNCO dimers and trimers were optimized at the MP2, B3LYPD3 and B2PLYPD3 levels of theory employing the 6-311++G(3df,3pd) basis set. Topological analysis of the electron density (AIM) was used to identify the type of non-covalent interactions in the studied aggregates. Five stable minima were located on the potential energy surface for (HNCO)₂, and nine were located on the potential energy surface for (HNCO)₃. The most stable dimer (D1) involves a weak, almost linear N-H⋯N hydrogen bond. Other structures are bound by a N-H⋯O hydrogen bond or by O⋯C or N⋯N van der Waals interactions. Similar types of interactions as in (HNCO)₂ were found in the case of HNCO trimers. Among nine stable (HNCO)₃ structures, five represent cyclic forms. The most stable T1 trimer structure is characterized by a six-membered ring formed by three N-H⋯N hydrogen bonds and representing high symmetry (C_3h). The analysis of the HNCO/Ar spectra after deposition indicates that the N-H⋯O hydrogen-bonded dimers are especially prevalent. Upon annealing, HNCO trimers were observed as well. Identification of the experimentally observed species relied on previous experimental data on HNCO complexes as well as computed data on HNCO homoaggregates' vibrational spectra.

Zigzag-Edged Polycyclic Aromatic Hydrocarbons from Benzo[m]tetraphene Precursors

A series of zigzag-edged polycyclic aromatic hydrocarbons (PAHs) (Z1-Z3) were synthesized from 2,12-dibromo-7,14-diphenyl-benzo[m]tetraphene (9) as a versatile building block. Their structures were unambiguously confirmed by laser desorption/ionization time-of-flight mass spectrometry, ¹ H NMR, Raman, and Fourier-transformed infrared (FTIR) spectroscopies as well as scanning tunneling microscopy. The fingerprint vibrational modes were elucidated with theoretical support. The edge- and size-dependent optical properties were characterized by UV-Vis absorption and fluorescence spectroscopy and DFT calculations. Moreover, ultrafast transient absorption spectroscopy revealed distinct modulation of the photophysical properties upon π-extension from Z1 to Z2, the latter having a gulf edge.

Silver Nanostar-Based SERS for the Discrimination of Clinically Relevant Acinetobacter baumannii and Klebsiella pneumoniae Species and Clones

The development of rapid, reliable, and low-cost methods that enable discrimination among clinically relevant bacteria is crucial, with emphasis on those listed as WHO Global Priority 1 Critical Pathogens, such as carbapenem-resistant Acinetobacter baumannii and carbapenem-resistant or ESBL-producing Klebsiella pneumoniae. To address this problem, we developed and validated a protocol of surface-enhanced Raman spectroscopy (SERS) with silver nanostars for the discrimination of A. baumannii and K. pneumoniae species, and their globally disseminated and clinically relevant antibiotic resistant clones. Isolates were characterized by mixing bacterial colonies with silver nanostars, followed by deposition on filter paper for SERS spectrum acquisition. Spectral data were processed with unsupervised and supervised multivariate data analysis methods, including principal component analysis (PCA) and partial least-squares discriminant analysis (PLSDA), respectively. Our proposed SERS procedure using silver nanostars adsorbed to the bacteria, followed by multivariate data analysis, enabled differentiation between and within species. This pilot study demonstrates the potential of SERS for the rapid discrimination of clinically relevant A. baumannii and K. pneumoniae species and clones, displaying several advantages such as the ease of silver nanostars synthesis and the possible use of a handheld spectrometer, which makes this approach ideal for point-of-care applications.

In Vitro Diagnosis and Visualization of Cerebral Ischemia/Reperfusion Injury in Rats and Protective Effects of Ferulic Acid by Raman Biospectroscopy and Machine Learning

Ischemic stroke is a major cause of mortality with complicated pathophysiological mechanisms, and hematoxylin and eosin (HE) staining is a histochemical diagnosis technique heavily relying on subjective observation. In this study, we developed a noninvasive assay using Raman spectroscopy for in vitro diagnosis and visualization of cerebral ischemia/reperfusion injury and protective effects of ferulic acid. By establishing a middle cerebral artery occlusion (MCAO) model in Sprague-Dawley male rats, we found effective interventions by ferulic acid using the neurological function score and HE staining. Raman spectra of neuronal and neuroglial cells exhibited significant intensity changes of protein, nucleotide, lipid, and carbohydrate at 780, 814, 1002, 1012, 1176, 1224, 1402, 1520, 1586, 1614, and 1752 cm^-1. Cluster vector analysis highlighted the alterations at 1002, 1080, 1298, 1430, 1478, 1508, 1586, and 1676 cm^-1. To evaluate the levels of neuron injury and intervention performance, a random forest model was developed on Raman spectral data and achieved satisfactory accuracy (0.9846), sensitivity (0.9679-0.9932), and specificity (0.9945-0.9989), ranking peaks around 1002 cm^-1 as key fingerprint for classification. Spectral phenylalanine-to-tryptophan ratio was the biomarker to visualize neuronal injury and intervention performance of ferulic acid with a resolution of 1 μm. Our results unravel the biochemical changes in neuronal cells with cerebral ischemia/reperfusion injury and ferulic acid treatment, and prove Raman spectroscopy coupled with machine learning as a power tool to classify neuron viability and evaluate the intervention performance in pharmacological research.

Terahertz Time-Domain Spectroscopy in Reflection Configuration for Inorganic and Mineral Pigment Identification

This work demonstrates terahertz time-domain spectroscopy (THz-TDS) in reflection configuration on a class of inorganic and mineral pigments. The technique is validated for pictorial materials against the limitations imposed by the back-reflection of the THz signal, such as weak signal intensity, multiple signal losses and distortion, as well as the current scarce databases. This work provides a detailed description of the experimental procedure and method used for the determination of material absorption coefficient of a group of 10 pigments known to be used in ancient frescoes, that are, Cu-based (azurite, malachite, and Egyptian blue), Pb-based (minium and massicot), Fe-based (iron oxide yellow, dark ochre, hematite, and Pompeii red) pigments and mercury sulfide (cinnabar), and classified the vibrational modes of the molecular oxides and sulfides for material identification. The results of this work showed that the mild signal in reflection configuration does not limit the application of THz-TDS on inorganic and mineral pigments as long as (i) the THz signal is normalized with a highly reflective reference sample, (ii) the secondary reflected signals from inner interfaces are removed with a filtering procedure, and (iii) the limitations at high frequencies imposed by the dynamic range of the instrument are considered. Under these assumptions, we were able to differentiate molecular phases of the same metal and identify azurite, Egyptian blue, minium, and cinnabar, isolating the molecular vibrations up to 125 cm^-1. The established approach demonstrated to be reliable, and it can be extended for the study of other materials, well beyond the reach of the heritage domain.

Quantitative Determination of Polyphenols and Flavonoids in Cistus × incanus on the Basis of IR, NIR and Raman Spectra

Cistus is a plant that has been used in natural medicine for hundreds of years; it works primarily as an antioxidant and cleansing agent. Cistus × incanus leaves or herb can be an attractive source of polyphenols and flavonoids. The official protocols of active compound analysis relies on the extraction of compounds of interest from plant matter, which makes their determination long and costly. An analysis of plant material in its native state can be performed using vibrational spectroscopy. This paper presents a comparison of Raman spectroscopy, attenuated total reflection in mid-infrared and diffuse reflectance technique in the near-infrared region for the simultaneous quantification of total polyphenols (TPC) and flavonoids (TF) content, as well as the determination of FRAP antioxidant activity of C. incanus material. Utilizing vibrational spectra and using partial least squares algorithm, TPC and TF were quantified with the RSEP_VAL errors in the 2.7-5.4% range, while FRAP antioxidant activity for validation sets was determined with relative errors ranged from 5.2 to 9.3%. For the analyzed parameters, the lowest errors of predictions were computed for models constructed using Raman data. The developed models allow for fast and precise quantification of the studied active compounds in C. incanus material without any chemical sample treatment.

Tracking water dimers in ambient nanocapsules by vibrational spectroscopy

Nanoconfined few-molecule water clusters are invaluable systems to study fundamental aspects of hydrogen bonding. Unfortunately, most experiments on water clusters must be performed at cryogenic temperatures. Probing water clusters in noncryogenic systems is however crucial to understand the behavior of confined water in atmospheric or biological settings, but such systems usually require either complex synthesis and/or introduce many confounding external bonds to the clusters. Here, we show that combining Raman spectroscopy with the molecular nanocapsule cucurbituril is a powerful technique to sequester and analyze water clusters in ambient conditions. We observe sharp peaks in vibrational spectra arising from a single rigid confined water dimer. The high resolution and rich information in these vibrational spectra allow us to track specific isotopic exchanges inside the water dimer, verified with density-functional theory and kinetic population modeling. We showcase the versatility of such molecular nanocapsules by tracking water cluster vibrations through systematic changes in confinement size, in temperatures up to 120° C, and in their chemical environment.